Recombination of rapidly evolving RNA-viruses provides an important mechanism for diversification, spread, and emergence of new variants with enhanced fitness. Foot-and-mouth disease virus (FMDV) causes an important transboundary disease of livestock that is endemic to most countries in Asia and Africa. Maintenance and spread of FMDV are driven by periods of dominance of specific viral lineages. Current understanding of the molecular epidemiology of FMDV lineages is generally based on the phylogenetic relationship of the capsid-encoding genes, with less attention to the process of recombination and evolution of non-structural proteins. In this study, the putative recombination breakpoints of FMDVs endemic to Southeast Asia were determined using full-open reading frame sequences. Subsequently, the lineages' divergence times of recombination-free genome regions were estimated. These analyses revealed a close relationship between two of the earliest endemic viral lineages that appear unrelated when only considering the phylogeny of their capsid proteins. Contrastingly, one lineage, named O/CATHAY, known for having a particular host predilection (pigs) has evolved independently. Additionally, intra-lineage recombination occurred at different breakpoints compared to the inter-lineage process. These results provide new insights about FMDV recombination patterns and the evolutionary interdependence of FMDV serotypes and lineages.
Bibliographical noteFunding Information:
This work was funded in part by ARS-CRIS Project 1940-32000-061-00D and through an interagency agreement with the Science and Technology Directorate of the U.S. Department of Homeland Security under Award Number HSHQDC-12-X-0060. Additional funding was provided by the Cooperative Biological Engagement Program of the U.S. Department of Defense, Defense Threat Reduction Agency. The work contributed by the WRLFMD was supported by the Department for Environment, Food and Rural Affairs (Project SE2943: Defra, UK), and funding provided to the EuFMD from the European Union. Barbara Brito, was the recipient of a Plum Island Animal Disease Center Research Participation Program fellowship, administered by the Oak Ridge Institute for Science and Education (ORISE) through an interagency agreement between the U.S. Department of Energy (DOE) and the U.S. Department of Agriculture (USDA). All opinions expressed in this paper are the authors’ and do not necessarily reflect the policies and views of the USDA-ARS FADRU, Vietnam DAH, WRLFMD or ORAU/ORISE. The Vietnam DAH, WRLFMD (The Pirbright Institute) and USDA-ARS FADRU are members of the Global Foot-and-Mouth Disease Research Alliance (GFRA).